Preheat the oven at 350 degrees F (about 177degrees C).
Prepare the muffin tin by greasing it with some melted coconut oil or lining it with muffin liners.
Using a medium-sized bowl, combine the dry ingredients - almond flour, coconut flour, pumpkin pie spice, baking powder, baking soda, psyllium husk, granulated monk fruit sweetener, and salt.
In another bowl, prepare the wet ingredients by whisking eggs, pumpkin puree, apple cider vinegar, coconut oil, almond milk, and vanilla extract.
Slowly add the dry ingredients into the bowl with the wet ingredients and combine properly until you obtain a nice smooth batter. Bear in mind that the dough will be slightly firm, and not as runny.
Using an ice-cream scoop or a spoon, fill each muffin liner about halfway with batter. Place some of the frosting in the middle then top again with the rest of the batter. Scoop any leftover cheese filling on top. If you like, use a toothpick to make swirls on the surface. I like to sprinkle some pumpkin pie spice on top, just before popping them in the oven.
Bake for about 20-30 minutes or until the tops turn golden brown and a toothpick inserted at the center comes out clean.
Serve the keto pumpkin cream cheese muffins with a cup of coffee or tea for breakfast, or enjoy them as a healthy snack.